Research Senior Scientist AI/ML Foundational Models

Role Summary

Senior Scientist to develop and deploy foundational AI models that transform drug discovery across Takeda. Build large-scale models (LLMs, diffusion models, multimodal architectures) integrating diverse data types—omics, biomedical imaging, protein 3D structures, and molecular representations. This role requires deep expertise in modern deep learning architectures combined with foundational knowledge of biology, chemistry, and disease biology to ensure models are scientifically grounded and impactful. You will train models from scratch, fine-tune pre-trained models for Takeda-specific applications, and deploy foundation model capabilities that accelerate discovery across all therapeutic platforms. Based in Boston, MA (Cambridge, MA area).

Responsibilities

• Develop and train foundational AI models (LLMs, diffusion models, flow-matching architectures) for drug discovery applications, with capability to pre-train on large-scale scientific corpora and molecular datasets.
• Fine-tune and adapt pre-trained foundation models (protein language models, chemical LLMs, vision transformers) for Takeda-specific applications in target identification, disease modeling, and molecular design and discovery.
• Build multimodal foundation models integrating diverse data types including omics (genomics, transcriptomics, proteomics), biomedical imaging, protein 3D structures, and molecular representations.
• Apply and extend state-of-the-art approaches including graph neural networks, transformer-based protein language models, and multimodal learning frameworks.
• Apply domain expertise in biology, chemistry, and/or disease biology to guide model architecture decisions, training data curation, and evaluation strategies ensuring scientific validity.
• Implement state-of-the-art generative architectures (diffusion, score-based models, autoregressive transformers) for molecular generation, protein design, and multi-objective optimization.
• Collaborate with computational scientists across domains to deploy foundation models that address diverse discovery needs across small molecules, biologics, and emerging modalities.
• Stay current with advances in foundation models, generative AI, and multimodal learning; contribute to internal knowledge sharing and external publications.

Qualifications

• Education: PhD in Computer Science, Machine Learning, Computational Biology, Bioinformatics, or related field with 2+ years relevant experience, OR MS with 6+ years relevant experience.
• Required: Deep expertise in modern deep learning architectures including transformers, diffusion models, and/or generative models.
• Required: Strong experience training large-scale models with proficiency in PyTorch and distributed training frameworks.
• Required: Foundational knowledge of biology, chemistry, or disease biology sufficient to guide scientifically meaningful model development.
• Required: Experience with at least one of protein language models (ESM, ProtTrans), molecular generative models, or biomedical vision models.
• Required: Experience with cloud computing (AWS, GCP) and GPU cluster training at scale.
• Preferred: Experience building or fine-tuning foundation models in pharmaceutical or life sciences settings.
• Preferred: Expertise in multimodal learning integrating text, images, and structured molecular data.
• Preferred: Experience with omics data analysis (genomics, transcriptomics, proteomics) and knowledge graph.
• Preferred: Familiarity with protein structure prediction and 3D molecular representations.
• Preferred: Publications in top-tier ML venues (NeurIPS, ICML, ICLR) or computational biology journals.
• Preferred: Experience with model compression, efficient inference, or production deployment of large models.
• Preferred: Strong background in large-scale data integration and multimodal modeling for biological systems.
• Preferred: Proficiency in Python and ML libraries (PyTorch, TensorFlow, scikit-learn); familiarity with Unix tools.
• Preferred: Excellent collaboration and communication skills.

Skills

• Ability to lead cross-functional initiatives and mentor junior scientists.
• Experience in translating computational insights into experimental strategies.
• Strong publication record or demonstrated thought leadership in AI for biology and molecular design.
• Comfort working in fast-paced, innovation-driven environments with evolving priorities.

Education

• PhD in Computer Science, Machine Learning, Computational Biology, Bioinformatics, or related field with 2+ years relevant experience, OR MS with 6+ years relevant experience.